Personally, I would render the left/right images to 2 different render-targets. Then I would use a pixel shader that checks the current pixel's position, and then samples either the left/right texture depending on if the position is odd/even.

If I recall correctly, there was an article on interlaced rendering in one of the original ShaderX books, which I think are available online for free. Try searching around for it - the technology may be outdated, but the theory should be more or less the same (interlaced video has been around since TV broadcasts started...).